XPFS: A new parallel PROSITE profile search algorithm on Xeon Phi

PROSITE provides rich documentation entries describing protein domains, families and functional sites, associated patterns as well as generalized profiles to identify them. Generalized profiles in PROSITE are often used to detect distantly related proteins by doing sequence comparison. The developments of the PROSITE have increased the discriminatory power of generalized profiles. However in practice, comparing PROSITE profiles to large protein databases, such as GenBank, usually requires long runtimes on sequential architectures. Due to the continuing rapid growth of sequence databases, there is a high demand to accelerate this task. In this paper we present XPFS, a new parallel algorithm for searching generalized profiles against protein sequence databases based on Xeon Phi which is Intel´s first generation Many Integrated Core product. To our knowledge this is the first reported implementation of the PROSITE profile search algorithm on Xeon Phi. The executable binary code of XPFS is available at http://xpfs.sdu-hpcl.org/.